We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.
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European Nucleotide Archive
All sequence data have been submitted to the European Nucleotide Archive (ENA) and are available under the following Ust’-Ishim accession number: PRJEB6622. The data from the 25 present-day human genomes are available from (http://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project/) and from (http://cdna.eva.mpg.de/neandertal/altai/).
We are grateful to P. Gunz, M. Kircher, A. I. Krivoshapkin, P. Nigst, M. Ongyerth, N. Patterson, G. Renaud, U. Stenzel, M. Stoneking and S. Talamo for valuable input, comments and help; T. Pfisterer and H. Temming for technical assistance. Q.F. is funded in part by the Chinese Academy of Sciences (XDA05130202) and the Ministry of Science and Technology of China (2007FY110200); P.A.K. by Urals Branch, Russian Academy of Sciences (12-C-4-1014) and Y.V.K. by the Russian Foundation for Basic Sciences (12-06-00045); F.J. and M.S. by the National Institutes of Health of the USA (R01-GM40282); P.J. by the NIH (K99-GM104158); and T.F.G.H. by ERC advanced grant 324139. D.R. is a Howard Hughes Medical Institute Investigator and supported by the National Science Foundation (1032255) and the NIH (GM100233). Major funding for this work was provided by the Presidential Innovation Fund of the Max Planck Society.
This file contains Supplementary Information Sections 1-18 – see Supplementary Contents for details
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BMC Evolutionary Biology (2018)